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Rant: Whenever I hear バタフライ効果, I cannot help imagining a swimmer, although I know that バタフライ in this context means the insect, not the swimming style. Whoever translated “butterfly effect” as バタフライ効果 for the first time (rather than something like 蝶の効果) should indemnify me for imprinting this false connection.
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Tsuyoshi ItoAug 11 '12 at 22:02

2 Answers
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From my experience, 蝶々 is the most used and recognized. Although I've never heard the pronunciation shortened to チョウチョ.

I personally like to use 胡蝶 (note: can also be written as 蝴蝶) because 1) it sounds cooler, and 2) 蝴蝶隠れ. But whenever I've used 蝴蝶 in conversation with my Japanese friends, none of them knew what I what talking about until I changed it to 蝶々.

I agree with your first paragraph. I wondered if 蝶々 was childish but I am told its not, just casual. 蝶 is more formal/固い. 胡蝶 seems to used for butterfly shaped flowers [胡蝶胡蝶草 butterfly flower《植物》〔花の形がチョウに似ている。),胡蝶蘭 Phalaenopsis orchid 黄胡蝶 dwarf poinciana《植物》- (Revised to match Tsuyoshi Ito's explanation to me-see below.)
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TimAug 12 '12 at 7:08

To be honest, I have never heard 蝶々 pronounced as ちょうちょう except in the name 蝶々夫人 (Madama Butterfly).
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Tsuyoshi ItoAug 13 '12 at 13:11

This is sort of a piggy-back/solidification of the first response [the one about Latin and whatnot], and also a clarification of the shortening.
** Also, sorry if you know some of this, or if it seems long-winded**

In terms of the shortening, this occasionally happens in colloquialism. Just as we shorten or slur words in more relaxed communication, this also happens in Japanese. So in terms of which one is safest to use, use ちょうちょう. If you look at an online dictionary (personally I like to use tangorin.com), they sometimes tell you which one is more common. The elongated one is more common, most likely because it is the one that is more socially acceptable and safe. You may hear the shortened form in very casual speech, but it shouldn't be used with just anyone as it can be disrespectful. You also wouldn't write the shortened version (unless in a super casual setting).

The choice between using 蝶 and 蝶々 is explained when you think about how kanji works. Kanji in itself is not a set of words, it is a set of meanings. so the kanji by itself means butterfly, but can be thought of as the butterfly nature of something. This is why you can have some words that can have the kanji for butterfly in it, and not refer to the insect (like 蝶ナート, which is a nut with a butterfly-ish form). So, think of 蝶々 as a "butterfly, butterfly" referring to the actual insect just as we would make such clarifications in English.

In terms of 胡蝶, it refers to the insect as well, but it is an archaic word. You will probably read it in novels more than you will hear it.

バタフライ would be used for an imported form of typing (imported because it is written in katakana, typing because of its usage). You can think of the difference between 蝶 and バタフライ can be thought of like this:

"Hey, I've got this new think/concept from America! It's called the Butterfly _!" (here you would use katakana)

"Hmmm, you know, I'm trying to come up with a name for this thing, and it kind of has the nature of a butterfly. I think i will call it chou__/_chou! " (in this case it would be kanji)

Of course this example can only be generalized, and some things are surely a case by case basis, but this should help I think.

@Tim: I am not a biologist, but as far as I know, calling a butterfly 胡蝶 is archaic. A butterfly is 蝶 even in biology (more precisely, it is チョウ because names of animals and plants are usually written in katakana in biology). I doubt that 胡蝶 is used in the 和名 of any species of butterflies, but I am not sure. There are some non-archaic words which contain 胡蝶 as their part, such as コチョウラン (胡蝶蘭; Phalaenopsis), and they were probably coined before the word 胡蝶 became archaic.
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Tsuyoshi ItoAug 12 '12 at 1:43